Chemistry Commons^™

Spectroscopy And Dynamics Of The Predissociated, Quasi-Linear S2 State Of Chlorocarbene, Chong Tao, Craig A. Richmond, Calvin Mukarakate, S. H. Kable, Eric C. Brown, Richard Dawes, Phalgun Lolur, Scott A. Reid

Chemistry Faculty Research and Publications

In this work, we report on the spectroscopy and dynamics of the quasi-linear S₂ state of chlorocarbene, CHCl, and its deuterated isotopologue using optical-optical double resonance (OODR) spectroscopy through selected rovibronic levels of the S₁ state. This study, which represents the first observation of the S₂ state in CHCl, builds upon our recent examination of the corresponding state in CHF, where pronounced mode specificity was observed in the dynamics, with predissociation rates larger for levels containing bending excitation. In the present work, a total of 14 S₂ state vibrational levels with angular momentum ℓ = 1 …

Potential Energy And Dipole Moment Surfaces Of Hco- For The Search Of H- In The Interstellar Medium, M. Ayouz, I. Mikhailov, Dmitri Babikov, M. Raoult, S. Galtier, O. Dulieu, V. Kokoouline

Chemistry Faculty Research and Publications

Potential energy and permanent dipole moment surfaces of the electronic ground state of formyl negative ion HCO− are determined for a large number of geometries using the coupled-cluster theory with single and double and perturbative treatment of triple excitations ab initio method with a large basis set. The obtained data are used to construct interpolated surfaces, which are extended analytically to the region of large separations between CO and H− with the multipole expansion approach. We have calculated the energy of the lowest rovibrational levels of HCO− that should guide the spectroscopic characterization of HCO− in laboratory experiments. The study …

Polysaccharide Ecocomposite Materials: Materials: Synthesis, Characterization And Application For Removal Of Pollutants And Bacteria, Simon Duri, Bilal El-Zahab, Chieu D. Tran

Chemistry Faculty Research and Publications

A novel, simple and totally recyclable method has been developed for the synthesis of nontoxic, biocompatible and biodegradable composite materials from cellulose and chitosan. In this method, [BMIm+Cl-], an ionic liquid (IL), was used as a solvent to dissolve and synthesize the [CEL+CS] composite materials. Since the IL can be removed from the materials by washing them with water, and recovered from the washed solution, the method is totally recyclable. XRD, FTIR, NIR and SEM were used to characterize the materials and to confirm that CEL and CS were successfully regenerated by the method without any chemical transformation. More importantly, …

A Chemical Proteomic Probe For Detecting Dehydrogenases: Catechol Rhodanine, Xia Ge, Daniel S. Sem

Chemistry Faculty Research and Publications

The inherent complexity of the proteome often demands that it be studied as manageable subsets, termed subproteomes. A subproteome can be defined in a number of ways, although a pragmatic approach is to define it based on common features in an active site that lead to binding of a common small molecule ligand (ex. a cofactor or a cross-reactive drug lead). The subproteome, so defined, can be purified using that common ligand tethered to a resin, with affinity chromatography. Affinity purification of a subproteome is described in the next chapter. That subproteome can then be analyzed using a common ligand …

Nmr Line Shapes And Multi-State Binding Equilibria, Evgenii L. Kovrigin

Chemistry Faculty Research and Publications

Biological function of proteins relies on conformational transitions and binding of specific ligands. Protein-ligand interactions are thermodynamically and kinetically coupled to conformational changes in protein structures as conceptualized by the models of pre-existing equilibria and induced fit. NMR spectroscopy is particularly sensitive to complex ligand-binding modes—NMR line-shape analysis can provide for thermodynamic and kinetic constants of ligand-binding equilibria with the site-specific resolution. However, broad use of line shape analysis is hampered by complexity of NMR line shapes in multi-state systems. To facilitate interpretation of such spectral patterns, I computationally explored systems where isomerization or dimerization of a protein (receptor) molecule …

Charge Delocalization In Self-Assembled Mixed-Valence Aromatic Cation Radicals, Tushar Navale, Khushabu Thakur, Vijay Vyas, Shriya Wadumethrige, Ruchi Shukla, Sergey V. Lindeman, Rajendra Rathore

Chemistry Faculty Research and Publications

The spontaneous assembly of aromatic cation radicals (D^+•) with their neutral counterpart (D) affords dimer cation radicals (D₂^+•). The intermolecular dimeric cation radicals are readily characterized by the appearance of an intervalence charge-resonance transition in the NIR region of their electronic spectra and by ESR spectroscopy. The X-ray crystal structure analysis and DFT calculations of a representative dimer cation radical (i.e., the octamethylbiphenylene dimer cation radical) have established that a hole (or single positive charge) is completely delocalized over both aromatic moieties. The energetics and the geometrical considerations for the formation …

Total Synthesis Of A Virotoxin And Analogs For Conformational Studies, Benson Jumba Edagwa

LSU Doctoral Dissertations

This dissertation describes the first total synthesis of alloviroidin in trace amounts, along with that of three analogs containing L-proline (Pro), trans-3-hydroxyproline (3-Hyp) or cis-4-hydroxyproline (4-hyp) residue substituting for 2,3-trans-3,4-trans-dihydroxyproline in the natural product. We report herein an efficient strategy that provides a dipeptide containing a (2S,4S)-4,5-dihydroxyleucine (dihyLeu) residue, including a diastereoselective dihydroxylation. Nα-Carbobenzyloxy-(2S)-4,5-dehydroleucine was coupled with valine ethyl ester to give a dipeptide that was subjected to a Sharpless asymmetric dihydroxylation to introduce the diol. The relative configuration at C4 was assigned as S by X-ray crystallography after derivatization as an α-amino-γ-lactone hydrochloride salt. The preparation of the 2-(methylsulfonyl)tryptophan …

Development Of Innovative Stationary Phases For Chiral And Protein Separations In Open Tubular Capillary Electrochromatography, Leonard Moore, Jr.

LSU Doctoral Dissertations

Protein biomarkers in bodily fluids can lead to an indication of the onset of a disease. Due to low abundance of the biomarker at early stages of the disease and other protein interferences, detection may be challenging. Therefore, in order to achieve more selective protein separations, the development of a novel stationary phase has been investigated. Moreover, novel methods to apply polysaccharides as stationary phases were developed for protein separations as well as chiral separations. The initial discussions in this dissertation commences with the use of novel zwitterionic lysine-based molecular micelles as a coating for open tubular capillary electrochromatography (OT-CEC) …

Challenges In The Discovery And Characterization Of Magnetic Intermetallics, William A. Phelan

LSU Doctoral Dissertations

The crystal growth and characterization of four families of compounds, LnFeSb3 (Ln = Pr, Nd, Sm, Gd, and Tb) and CeCo(Sb, Sn)3, Ln2Fe4Sb5 (Ln = La – Nd and Sm), LnCu2(Al,Si)5 (Ln = La and Ce), and Ln(Cu,Al,Ga)13 (Ln = La – Pr and Eu), are presented in this dissertation. Special emphasis is placed on describing their structure-magnetic properties correlations. Discoveries and studies of these systems were motivated by their structurally related predecessors, which are comprised of complex structural subunits and exhibit unusual physical properties. The magnetic behaviors exhibited by a selection of these intermetallics include the large magnetoresistances and …

Infrared Laser Ablation For Biological Mass Spectrometry, Fan Huang

LSU Doctoral Dissertations

Instrument and technique development and modeling of ionization methods using infrared (IR) laser desorption and ablation for mass spectrometry (MS) analysis of chemical and biochemical samples are described. Infrared lasers are highly efficient at sample removal and post-ablation ionization of materials removed by IR laser can be used to improve ionization efficiency. Fundamental studies of the physical processes in laser ablation mass spectrometry can help elucidate the mechanism. In this research, an infrared/ultraviolet two-laser matrix-assisted laser desorption ionization (MALDI) MS was developed for analysis of biomolecules. An infrared laser was used to ablate a mixture of analyte and matrix, and …

Synthesis, Characterization, And Self-Assembly Of Porphyrins Conjugated To Superparamagnetic Colloidal Particles For Enhanced Photodynamic Therapy, Javoris Hollingsworth

LSU Doctoral Dissertations

Porphyrins and their derivatives are often used as photosensitizers in photodynamic therapy (PDT), which is a noninvasive antitumor treatment. The photochemical process for PDT involves exciting a photosensitizing agent with visible light, which induces cytotoxicity in the presence of oxygen as a result of forming reactive oxygen species (ROS). The ROS are the responsible components for invoking cell death and destruction of tumors. Although this mechanism is an effective cancer therapeutic, it still has many shortcomings. One major challenge of PDT concerns improving the tumor selectivity and specificity of photosensitizers because porphyrins have nonspecific affinity to tumor cells. The discussed …

Atr-Ftir Studies On The Kinetics Of Dimethylarsinic Acid (Dma) Surface Complexation With Iron(Oxyhydr)Oxides, Julia Tofan-Lazar Miss

Theses and Dissertations (Comprehensive)

Dimethylarsinic acid (DMA) is an organoarsenical compound that, along with monomethylarsonic acid, poses a health and an environmental risk, and a challenge to the energy industry. Little is known about the surface chemistry of DMA at the molecular level with materials relevant to geochemical environments and industrial sectors. The surface chemistry of phosphorus and arsenic compounds in their organic and inorganic forms is of great interest due to its role in controlling their transport, bioaccessibility and speciation. This thesis reports the first in-situ and surface-sensitive rapid kinetic studies on the adsorption and desorption of DMA to and from Fe-(oxyhydr)oxide films …

Synthesis And Investigation Of The Liquid Crystalline Properties Of Polycyclic Aromatic Hydrocarbons, Joseph A. Paquette

Theses and Dissertations (Comprehensive)

In this thesis, the synthesis and liquid crystalline properties of a series of novel substituted dibenz[a,c]anthracenes is reported. Specifically, a series of hexaalkoxydibenz[a,c]anthracenes were prepared and found not to exhibit a mesophase. In contrast, when substituents are introduced on the aromatic core, columnar mesophases are observed over broad temperature ranges. A series substituted derivatives was prepared and their mesomorphic properties compared. In general, electron-withdrawing substituents promote broad mesophase temperature ranges, as do larger substituents. The liquid crystalline phase is a result of the electronic effects, size and shape of the substituents in the 10 and 13 positions.

We also synthesized …

Laboratory Methods For The Advancement Of Wastewater Treatment Modeling, Holly E. Gray

Theses and Dissertations (Comprehensive)

To achieve the low levels of total phosphorus required in wastewater treatment plant effluent all chemical forms of phosphorus should be removed. The most refractory phosphorus in terms of removal is so-called “organic phosphorus”. This thesis explores potential relationships between dissolved organic matter and organic phosphorus and methods of removing organic phosphorus from waste water. Fluorescence spectroscopy will be used to characterize dissolved organic matter (DOM) in wastewater. The fluorescent DOM will then be monitored throughout the various wastewater treatment plants to investigate any changes throughout the treatment train. Correlations between fluorophore concentrations (concentrations determined for the different classifications of …

Characterizing Dissolved Organic Matter And Cu2+, Zn2+, Ni2+, And Pb2+ Binding In Salt Water And Implications For Toxicity, Rachael L. Diamond

Theses and Dissertations (Comprehensive)

The binding of metal to dissolved organic matter in aquatic environments is important in controlling the bioavailability and potential toxicity of metals such as Zn²⁺, Pb²⁺, Ni²⁺ and Cu²⁺. The purpose of this research is to: (i) quantify binding capacity to different sources of marine organic matter at environmentally relevant concentrations; (ii) test fluorescence quenching and voltammetric method for use in seawater conditions and; (iii) compare predicted speciation parameters with toxicological observations in the same samples.

Information regarding the solubility of copper and copper compounds is important for risk assessment and can be …

Density Functional Theory Calculations On Hydrated Dimethylarsinic Acid And Iron Oxide Clusters, Adrian Adamescu

Theses and Dissertations (Comprehensive)

Dimethylarsinic Acid (DMA) or (CH₃)₂AsO₂H is an important organoarsenical compound detected in arsenic speciation studies of environmental samples and synthesized during pyrolysis of oil shale. DMA was used historically as a herbicide on large agricultural fields and can be detected in the leachates of landfills rich in waste containing arsenic such as glass, alloys, and semiconductors, as well as biologically pre-treated municipal solid waste. Under certain soil conditions DMA can become bio-available and has the potential to be recycled to more toxic inorganic forms of arsenic. Bioavailability of DMA is largely controlled by the …

A Novel Method Of Studying Ion Formation And Fragmentation Using A Modified Time-Of-Flight Mass Spectrometer, David S. Ames

Dissertations and Theses @ UNI

Laser desorption has been an important tool in mass spectrometry. It has been known that an order of magnitude more neutrals than ions are produced during laser desorption. A Time-Of-Flight Mass Spectrometer with an infinitely adjustable acceleration region was constructed to map the population distribution of neutral ion precursors and metastable ions in the flight tube. Desorption was performed by using a nitrogen UV laser at 337 nm. Experiments conclude that the majority of post-source ionization of neutrals occurs approximately 2.5 cm from the sample-laser interface. The intensity of ions tapers rapidly out to 6.0 cm, however ions were detected …

Chyd1 Solution Phase Synthesis Optimization And The Development Of A Novel Human Growth Hormone Antagonist And Agonist, Philip Murray

USF Tampa Graduate Theses and Dissertations

Inhibiting protein-protein interactions to achieve a therapeutically desired effect has been a goal in the field of drug discovery for decades. Recently, advances in peptidomimetics have led researches to the use of cyclized peptides to achieve this goal. Cyclization of linear peptides restricts the number of conformations of the peptide, increasing the peptide's affinity to binding to the desired target. Cyclization also stabilizes the peptide, allowing the peptide to be resistant to proteases. This study explores the optimization of solution phase synthesis of an important integrin-mediated cell adhesion cyclic peptide for the therapeutic inhibition of multiple myeloma, cHYD1. cHYD1 was …

Novel Blends Of Sulfur-Tolerant Water-Gas Shift Catalysts For Biofuel Applications, Timothy Michael Roberge

USF Tampa Graduate Theses and Dissertations

As traditional sources of energy become depleted, significant research interest has gone into conversion of biomass into renewable fuels. Biomass-derived synthesis gas typically contains concentrations of approximately 30 to 600 ppm H2S in stream. H2S is a catalyst poison which adversely affects downstream processing of hydrogen for gas to liquid plants. The water-gas shift reaction is an integral part of converting CO and steam to H2 and CO2. Currently, all known water-gas shift catalysts deactivate in sulfur concentrations typical of biomass-derived synthesis gas. Novel catalysts are needed to remain active in the presence of sulfur concentrations in order to boost …

Molecular Dynamics Of The Rna Binding Cavity Of Influenza A Non-Structural Protein 1 (Ns1) Rna Binding Domain, Christi Leigh Whittington

USF Tampa Graduate Theses and Dissertations

Molecular dynamics simulations were performed on the influenza A non-structural protein 1 (NS1) RNA binding domain (RBD), a homodimer. Fourteen simulations were performed at 298K, nine ionized with 0.1M KCl and five with no ions. Several analysis techniques were employed to study RBD residue flexibility. The focus of the study was the RNA binding cavity formed by side chains of helix 2 (chain A) and helix 2’ (chain B) and cavity intermonomeric salt bridges. Opening of the salt bridges D29–R46’ and D29’–R46 was observed in several of the trajectories. The RNA binding cavity has large flexibility, where the dimension and …

Asymmetric Intra- And Intermolecular Cyclopropanation By Co(Ii)- Based Metalloradical Catalysis, Xue Xu

USF Tampa Graduate Theses and Dissertations

Metal-catalyzed cyclopropanation of olefins with diazo reagents has attracted research interest because of its fundamental and practical importance. The resulting cyclopropyl units are recurrent motifs in biologically important molecules and can serve as versatile precursors in organic synthesis. Since they were first introduced in 2004, Co(II) complexes of D₂-symmetric chiral amidoporphyrins [Co(D₂-Por*)] have emerged as a new class of catalysts for asymmetric cyclopropanation. These metalloradical catalysts have been shown to be highly effective for asymmetric intermolecular cyclopropanation of a broad scope of substrates with different classes of carbene sources, particularly including electron-deficient olefins and acceptor/acceptor-substituted …

Drug Discovery From Floridian Mangrove Endophytes, Jeremy Beau

USF Tampa Graduate Theses and Dissertations

A significant challenge of the 21st century is the growing health threat stemming from drug-resistant infectious diseases. There is an undeniable need to discover new, safe and effective drugs with novel mechanisms of action to combat this threat. A study of drugs currently on the market showed that natural products account for approximately 75% of new anti-infective drugs, either as new agents or analogs based upon their structure. Unfortunately, major pharmaceutical companies have cut back tremendously in natural products research in part due to the frustrating obstacle of frequent rediscovery of compounds. Fungi in particular are difficult to work with …

Synthesis And Anti-Mrsa Activity Of Hydrophilic C3-Acylated N-Thiolated Β-Lactams And N-Acyl Ciprofloxacin-N-Thiolated Β-Lactam Hybrids, Biplob Bhattacharya

USF Tampa Graduate Theses and Dissertations

The Turos laboratory has been working with N-thiolated β-lactams for years trying to understand the mode of action and structural features it needs to have biological activity. Over the years new data has shown promising inhibitory activity against various microbes.

In this dissertation, a review of the vast amount of work carried out on N-thiolated β-lactams in Turos laboratory has been done and their novelty, in terms of structure and mechanism has been discussed. A complete outline of our work in the discovery and ongoing development of these compounds, starting from our initial, unexpected finding of antimicrobial activity for one …

Chiral Binol Metal Phosphate/Phosphoric Acid Catalyzed Enantioselective Addition Of Phosphorus And Sulfur Nucleophiles To Imines And Epoxides, Gajendrasingh Ingle

USF Tampa Graduate Theses and Dissertations

The research presented in this dissertation focuses on chiral BINOL metal phosphatephosphoric acid catalyzed enantioselective additions of phosphorus and sulfur nucleophiles to imines and epoxides. In chapter 2, we reported a new method to synthesize chiral amino phosphine oxides. The reaction combines N-substituted imines and diphenylphosphine oxide catalyzed by chiral magnesium 9-antryl phosphate. A wide variety of aliphatic and aromatic aldimines substituted by electron neutral benzhydryl or dibenzocycloheptene groups were excellent substrates for the addition reaction. The imines protected with dibenzocycloheptene protecting group provided better enantioselectivity than those protected with benzhydryl group, while both imines gave comparable yields. Also, …

Development And Optimization Of Kinetic Target-Guided Synthesis Approaches Targeting Protein-Protein Interactions Of The Bcl-2 Family, Sameer Shamrao Kulkarni

USF Tampa Graduate Theses and Dissertations

Kinetic target-guided synthesis (TGS) and in situ click chemistry are among unconventional discovery strategies having the potential to streamline the development of protein-protein interaction modulators (PPIMs). In kinetic TGS and in situ click chemistry, the target is directly involved in the assembly of its own potent, bidentate ligand from a pool of reactive fragments. Herein, we report the use and validation of kinetic TGS based on the sulfo-click reaction between thio acids and sulfonyl azides as a screening and synthesis platform for the identification of high-quality PPIMs. Starting from a randomly designed library consisting of nine thio acids and nine …

Design Of Colloidal Composite Catalysts For Co2 Photoreduction And For Co Oxidation, Bijith D. Mankidy

USF Tampa Graduate Theses and Dissertations

In this doctoral dissertation, novel colloidal routes were used to synthesize nanomaterials with unique features. We have studied the impact of nanoparticle size of catalyst, role of high surface area of a photocatalyst, and the effect of varying elemental composition of co-catalytic nanoparticles in combination with core-shell plasmonic nanoparticles. We have demonstrated how physical and chemical characteristics of nanomaterials with these unique features play a role in catalytic reactions, specifically the oxidation of CO and the photoreduction of CO2. The first objective of this doctoral dissertation involved the preparation of CoO nanoparticles with discrete nanoparticles sizes (1-14 nm) using a …

Enantioselective Brønsted And Lewis Acid-Catalyzed Reaction Methodology: Aziridines As Building Blocks For Catalytic Asymmetric Induction, Shawn E. Larson

USF Tampa Graduate Theses and Dissertations

Chiral molecules as with biological activity are plentiful in nature and the chemical literature; however they represent a smaller portion of the pharmaceutical drug market. As asymmetric methodologies grow more powerful, the tools are becoming available to synthesize chiral molecules in an enantioselective and efficient manner.

Recent breakthroughs in our understanding of phosphoric acid now allow for Lewis acid catalysis via pairing with alkaline earth metals. Using alkaline earth metals with chiral phosphates is an emerging approach to asymmetric methodology, but already has an influential record.

The development of new conditions for the phosphoric acid-catalyzed highly enantioselective ring-opening of meso-aziridines …

Development Of A Bio-Molecular Fluorescent Probe Used In Kinetic Target-Guided Synthesis For The Identification Of Inhibitors Of Enzymatic And Protein-Protein Interaction Targets, Katya Pavlova Nacheva

USF Tampa Graduate Theses and Dissertations

Abstract

Fluorescent molecules used as detection probes and sensors provide vital information about the chemical events in living cells. Despite the large variety of available fluorescent dyes, new improved fluorogenic systems are of continued interest. The Diaryl-substituted Maleimides (DMs) exhibit excellent photophysical properties but have remained unexplored in bioscience applications. Herein we present the identification and full spectroscopic characterization of 3,4-bis(2,4-difluorophenyl)-maleimide and its first reported use as a donor component in Forster resonance energy transfer (FRET) systems. The FRET technique is often used to visualize proteins and to investigate protein-protein interactions in vitro as well as in vivo. The analysis …

Design Of Novel Inhibitors For Infectious Diseases Using Structure-Based Drug Design: Virtual Screening, Homology Modeling And Molecular Dynamics, Divya Ramamoorthy

USF Tampa Graduate Theses and Dissertations

The main aim of the study in this thesis was to use structure-based protocols to design new drugs for enzymes, DXS and DXR in the non mevalonate pathway. Another aim of this study was to identify the dimer interface in E.coli FabH as an allosteric binding site for designing new class of anti-infective drugs. We have attempted to identify potential inhibitors for DXS by docking the NCI Diversity set compounds, compound libraries available from GSK-MMV and St. Jude's Children's research center. FabH dimer interface has been identified as a potential target using SiteMap, Alanine mutagenesis and docking studies.

The first …

Use And Development Of Computational Tools In Drug Discovery: From Small Molecules To Cyclic Peptides, Daniel Navarrete Santiago

USF Tampa Graduate Theses and Dissertations

The scope of this work focuses on computationally modeling compounds with protein structures. While the impetus of drug discovery is the innovation of new therapeutic molecules, it also involves distinguishing molecules that would not be an effective drug. This can be achieved by inventing new tools or by refining old tools. Virtual screening (VS, also called docking), the computational modeling of a molecule in a receptor structure, is a staple in predicting a molecule's affinity for an intended target. In our Virtual Target Screening system (also called inverse-docking), VS is used to find high-affinity targets, which can potentially explain absorption, …